AW: Assigning different temperatures to simulation

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Apr 02 2014 - 02:45:57 CDT

Didn't know about this langevinfile, good to know now. ;)

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: Jérôme Hénin [mailto:jerome.henin_at_ibpc.fr]
> Gesendet: Mittwoch, 2. April 2014 09:36
> An: Jhonatam Cordeiro Rodrigues
> Cc: Norman Geist; Namd Mailing List
> Betreff: Re: namd-l: Assigning different temperatures to simulation
>
> Hi Jhonatam,
>
> You want to:
> 1- thermalize everything at 300K
> 2- run a simulation with a thermostat at 400K acting only on the
> substrate. Do this by supplying a "langevinFile" with coefficients of
> zero for the liquid.
>
> Side remark, scaling velocities by 400/300 is wrong for two reasons.
> What are the two errors? Exercise to the reader. I'll be grading the
> answers.
>
> Cheers,
> Jerome
>
>
>
> ----- Mail original -----
> > Hi Norman
> >
> > Thank you for the answer, twice :). I decided to post it on the right
> > mailing list, as you suggested.
> >
> > Cordeiro
> >
> >
> >
> > On Wed, Apr 2, 2014 at 1:06 AM, Norman Geist <norman.geist_at_uni-
> greifswald.de
> > > wrote:
> >
> > > Little error in last post, this should work:
> > >
> > >
> > >
> > > set my400 [atomselect top "resid 1 to 10"]
> > >
> > > $my400 set {x y z} [vecscale [$my400 get {x y z}] [expr
> sqrt(400/300)]]
> > >
> > > $my400 delete
> > >
> > > set all [atomselect top all]
> > >
> > > $all writepdb "mymodifiedrestart.vel"
> > >
> > > $all delete
> > >
> > >
> > >
> > > Norman Geist.
> > >
> > >
> > >
> > > *Von:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu]
> *Im
> > > Auftrag von *Jhonatam Cordeiro Rodrigues
> > > *Gesendet:* Dienstag, 1. April 2014 22:30
> > > *An:* namd-l_at_ks.uiuc.edu
> > > *Betreff:* namd-l: Assigning different temperatures to simulation
> > >
> > >
> > >
> > > Hello
> > >
> > >
> > >
> > > How would be the proper way for me to assign different temperatures
> for
> > > different parts of my simulation. I'm trying to assign a
> temperature to a
> > > substrate (400K) while a liquid on top of it is initially at
> (300K), so
> > > that I can visualize how the liquid behave during the heat up.
> > >
> > >
> > >
> > >
> > >
> > > All the best
> > >
> > > Jhonatam Cordeiro
> > >
> > > Ph.D student
> > >
> > > NCA&T-Department of Industrial Engineering
> > >
> > >
> > > ------------------------------
> > > <http://www.avast.com/>
> > >
> > > Diese E-Mail ist frei von Viren und Malware, denn der avast!
> > > Antivirus<http://www.avast.com/>Schutz ist aktiv.
> > >
> > >
> >

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